%%% Seznam použité literatury je zpracován podle platných standardů. Povinnou citační
%%% normou pro bakalářskou práci je ISO 690. Jména časopisů lze uvádět zkráceně, ale jen
%%% v kodifikované podobě. Všechny použité zdroje a prameny musí být řádně citovány.

\def\bibname{Zoznam použitej literatúry}
\newcommand{\ts}{\textsuperscript}
% 2\ts{nd}~ed.

\begin{thebibliography}{99}
\addcontentsline{toc}{chapter}{\bibname}

\bibitem{branden98}
	{\sc Branden,} Carl-Ivan a {\sc Tooze,} John.
	\emph{Introduction to Protein Structure}.
	2.~edícia,
	pp. 3--5,
	New York: Garland Publishing, 1998.
	ISBN 0-8153-2304-2.

\bibitem{buxbaum07}
	{\sc Buxbaum,} Engelbert.
	\emph{Fundamentals of Protein Structure and Function}.
	New York: Springer Science+Business Media, LLC., 2007.
	ISBN 978-0-387-26352-6.
	
\bibitem{mcgraw98}
	{\sc Paolella,} Peter.
	\emph{Introduction to Molecular Biology, First Edition}.
	Pp. 51--58,
	USA: The McGraw-Hill Companies, Inc., 1998. 
	ISBN 0-697-20939-3.
	
\bibitem{raineri01}
	{\sc Raineri,} Deanna.
	\emph{Introduction to Molecular Biology}.
	Massachusetts: Blackwell Science, Inc., 2001.
	ISBN 0-632-04379-2.

\bibitem{hartl01}
	{\sc Hartl,} Daniel L. a {\sc Jones,} Elizabeth W.
	\emph{Genetics: Analysis of Genes and Genomes}.
	5. edícia,
	Massachusetts: Jones \& Bartlett Learning, 2001.
	ISBN 0-7637-0913-1.
	
\bibitem{whitford05}
	{\sc Whitford,} David.
	\emph{Proteins Structure and Function}.
	Strana 180,
	Chichester: John Wiley \& Sons Ltd, 2005.
	ISBN 0-471-49893-9.
	
\bibitem{hoksza10}
	{\sc Hoksza,} David.
	\emph{Similarity Search in Protein Databases}.
	Doktorská dizertácia,
	Katedra softwarového inženýrství Univerzity Karlovy, 2010.
	
\bibitem{engelbrecht07}
	{\sc Engelbrecht,} Andries P.
	\emph{Computational Intelligence: An Introduction}.
	2. edícia,
	Chichester: John Wiley \& Sons Ltd, 2007.
	ISBN 978-0-470-03561-0.
	
\bibitem{fogel03}	
	{\sc Fogel,} Gary B. a {\sc Corne,} David W.
	\emph{Evolutionary Computation in Bioinformatics}.
	USA: Elsevier Science, 2003.
	ISBN 1-55860-79-8.
	
\bibitem{koza98}
	{\sc Koza,} John R.
	\emph{Genetic Programming: on the Programming of Computers by Means of Natural Selection}.
	6. edícia,
	Massachusetts Institute of Technology, 1998.
	ISBN 0-262-11170-5.
	
\bibitem{singh00}
	{\sc Singh,} Amit P. a {\sc Brutlag,} Douglas L.
	\emph{Protein Structure Alignment: A Comparison of Methods} [online]. 2000,	[cit. 2012-11-15]. \\
	\url{http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.33.3694}.
	
\bibitem{mount01}
	{\sc Mount} D.W.
	\emph{Bioinformatics: Sequence and Genome Analysis}	.
	Prvá edícia,
	New York: Cold Spring Harbor Laboratory Press, 2001.
	ISBN 978-0879696085.
	
\bibitem{needleman70}
	{\sc Needleman,} S.B. a {\sc Wunsch,} C.D.
	\emph{A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins}.
	48(3): pp. 443–453, Journal of Molecular Biology, 1970. 
	ISSN 0022-2836.		
	
\bibitem{smith81}
	{\sc Smith,} T.F. a {\sc Waterman,} M.S.
	\emph{Identification of Common Molecular Subsequences}.
	147(1): pp. 195-7, Journal of Molecular Biology, 1981. 	
	
\bibitem{holm93}
	{\sc Holm,} L. a {\sc Sander}, C.
	\emph{Protein Structure Comparison by Alignment of Distance Matrices} [online]. 1993, [cit. 2012-11-17]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/8377180}.
	
\bibitem{gerstein96}
	{\sc Gerstein,} M. a {\sc Levitt,} M.
	\emph{Using Iterative Dynamic Programming to Obtain Accurate Pair-Wise and Multiple Alignments of Protein Structures} [online]. 1996, [cit. 2012-11-17]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/8877505}.
	
\bibitem{gibrat96}
	{\sc Gibrat,} J.F. a spol.
	\emph{Surprising Similarities in Structure Comparison} [online]. 1996, [cit. 2012-11-17]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/8804824}.
	
\bibitem{falicov96}
	{\sc Falicov,} A. a {\sc Cohen,} F.E.
	\emph{A Surface of Minimum Area Metric for the Structural Comparison of Proteins} [online]. 1996, [cit. 2012-11-17]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/8637017}.
	
\bibitem{singh97}
	{\sc Singh,} Amit P. a {\sc Brutlag,} Douglas L.
	\emph{Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations} [online]. 1997, [cit. 2012-11-17]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/9322051}.
	
\bibitem{ritchie12}	
	{\sc Ritchie,} D.W. a spol.
	\emph{Fast Protein Structure Alignment using Gaussian Overlap Scoring of Backbone Peptide Fragment Similarity} [online]. 2012, [cit. 2012-11-17]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/23093609}.
	
\bibitem{galgonek11}
	{\sc Galgonek,} J.; {\sc Hoksza,} D. a {\sc Skopal,} T.
	\emph{SProt: Sphere-Based Protein Structure Similarity Algorithm} [online]. 2011, [cit. 2012-11-17]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/22166105}.

\bibitem{szustakowski00}
	{\sc Szustakowski,} J.D. a {\sc Weng,} Z.
	\emph{Protein Structure Alignment Using a Genetic Algorithm} [online]. 2000, [cit. 2012-11-20]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/10707029}.
	
\bibitem{szustakowski02}
	{\sc Szustakowski,} J.D. a {\sc Weng,} Z.
	\emph{K2: Protein Structure Comparisons and Their Statistical Significancem} [online]. 2002, [cit. 2012-11-20]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/10707029}.
	
\bibitem{samuel59}
	{\sc Samuel,} A.L.
	\emph{Some Studies in Machine Learning Using the Game of Checkers}.
	3(3), pp. 210–229, IBM Journal of Research and Development, 1959.
	
\bibitem{henikoff92}
	{\sc Henikoff,} S. a {\sc Henikoff,} J.G.
	\emph{Amino Acid Substitution Matrices from Protein Blocks}.
	PNAS 89(22): pp. 10915–10919, 1992.
	
\bibitem{back96}	
	{\sc B\"{a}ck,} Thomas.
	\emph{Evolutionary Algorithms in Theory and Practice}.
	New York: Oxford University Press, 1996.
	ISBN 0-19-509971-0.
	
\bibitem{whitley89}
	{\sc Whitley,} Darrell.
	\emph{The GENITOR Algorithm and Selection Pressure: Why Rank-Based Allocation of Reproductive Trials is Best}.
	Pp. 116-121, Proceedings of the third international conference on Genetic algorithms, 1989.	
	
\bibitem{birzele07}
	{\sc Birzele,} F. a spol.
	\emph{Vorolign--Fast Structural Alignment Using Voronoi Contacts} [online].
	23(2): e205-11, Bioinformatics. 2007, [cit. 2012-11-30]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/17237093}.
		
\bibitem{chandonia04} 
	{\sc Chandonia,} J.M. a spol.
	\emph{The ASTRAL Compendium in 2004} [online].
	32(Database issue): D189-92, Nucleic Acid Res. 2004, [cit. 2012-11-30]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/14681391}.
	
\bibitem{hoksza10b}
	{\sc Hoksza,} D. a {\sc Galgonek,} J.
	\emph{Alignment-Based Extension to DDPIn Feature Extraction} [online].
	International Journal of Computational Bioscience. 2010, [cit. 2012-11-30]. \\
	\url{http://siret.ms.mff.cuni.cz/hoksza/papers/ijcb2010.pdf}.
	
\bibitem{sacan08}
	{\sc Sacan,} A.; {\sc Toroslu}, I.H.; {\sc Ferhatosmanoglu}, H.
	\emph{Integrated Search and Alignment of Protein Structures} [online].
	24(24), pp. 2872–2879, Bioinformatics. 2008, [cit. 2012-11-30]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/18945684}.

\bibitem{altschul97}
	{\sc Altschul,} S.F. a spol.
	\emph{Gapped BLAST and PSI-BLAST: a New Generation of Protein Database Search Programs} [online].
	25: pp. 3389–3402, Nucleic Acids Res. 1997, [cit. 2012-11-30]. \\
	\url{http://www.ncbi.nlm.nih.gov/pubmed/9254694}.
	
\bibitem{zhang04} 	
	{\sc Zhang,} Y. a {\sc Skolnick,} J.
	\emph{Scoring Function for Automated Assessment of Protein Structure Template Quality}.
	57(4): pp. 702-710, Proteins: Structure, Function, and Bioinformatics, 2004.
	
\bibitem{qt}
	\emph{Qt 4.7: Installation} [online]. c2008-2011, [cit. 2012-12-05]. \\
	\url{http://doc.qt.digia.com/4.7-snapshot/installation.html}.
	
%\bibitem{lamport94}
%  {\sc Lamport,} Leslie.
%  \emph{\LaTeX: A Document Preparation System}.
%  2. vydání.
%  Massachusetts: Addison Wesley, 1994.
%  ISBN 0-201-52983-1.

\end{thebibliography}
